resources/embl_mapping.xml

   1 <?xml version="1.0"?>\r
   2 <mapping xmlns="http://castor.exolab.org/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
   3         xsi:schemaLocation="http://castor.exolab.org/ castor-mapping.xsd">\r
   4         <!-- -->\r
   5         <class name="jalview.datamodel.xdb.embl.EmblFile">\r
   6                 <map-to xml="EMBL_Services"/>\r
   7                 <field name="entries" type="jalview.datamodel.xdb.embl.EmblEntry" collection="vector">\r
   8                         <bind-xml name="entry"/>\r
   9                 </field>\r
  10                 \r
  11                 <field name="errors" type="jalview.datamodel.xdb.embl.EmblError" collection="vector">\r
  12                         <bind-xml name="Error"/>\r
  13                 </field>\r
  14         </class>\r
  15         <class name="jalview.datamodel.xdb.embl.EmblEntry">\r
  16                 <map-to xml="entry"/>\r
  17                 <field name="accession" type="string">
  18                         <bind-xml location="accession" node="attribute"/>
  19                 </field>\r
  20                 <field name="lastUpdated" type="string">\r
  21                         <bind-xml location="last-updated" node="attribute"/>\r
  22                 </field>\r
  23                 <field name="version" type="string">\r
  24                         <bind-xml location="version" node="attribute"/>\r
  25                 </field>\r
  26                 \r
  27                 <field name="rCreated" type="string">\r
  28                         <bind-xml location="releaseCreated" node="attribute"/>\r
  29                 </field>\r
  30                 <field name="rLastUpdated" type="string">\r
  31                         <bind-xml location="releaseLastUpdated" node="attribute"/>\r
  32                 </field>\r
  33                 <field name="desc" type="string">
  34                         <bind-xml name="description" node="element"/>
  35                 </field>\r
  36                 <field name="Keywords" type="string" collection="vector">\r
  37                         <bind-xml name="keyword" node="element"/>\r
  38                 </field>\r
  39                 <field name="sequence" type="jalview.datamodel.xdb.embl.EmblSequence">\r
  40                         <bind-xml location="sequence" node="element"/>\r
  41                 </field>\r
  42                 <field name="features" type="jalview.datamodel.xdb.embl.EmblFeature" collection="vector">\r
  43                         <bind-xml name="feature"/>
  44                 </field>\r
  45                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">\r
  46                         <bind-xml name="dbreference" />\r
  47                 </field>\r
  48         </class>\r
  49         <class name="jalview.datamodel.xdb.embl.EmblSequence">
  50                 <map-to xml="sequence"/>\r
  51                 <field name="type" type="string">\r
  52                         <bind-xml name="type" node="attribute" location="type"/>\r
  53                 </field>\r
  54                 <field name="version" type="string">\r
  55                         <bind-xml name="version" node="attribute" location="version"/>\r
  56                 </field>\r
  57                 <field name="sequence" type="string">\r
  58                         <bind-xml node="text"/>\r
  59                 </field>
  60         </class>\r
  61         <class name="jalview.datamodel.xdb.embl.EmblFeature" verify-constructable="false">\r
  62                 <map-to xml="feature"/>\r
  63                 <field name="name" type="string">
  64                         <bind-xml name="name" node="attribute"/>
  65                 </field>\r
  66                 <field name="dbRefs" type="jalview.datamodel.DBRefEntry" collection="vector">
  67                         <bind-xml name="dbreference" node="element"/>
  68                 </field>\r
  69                 <field name="qualifiers" type="jalview.datamodel.xdb.embl.Qualifier" collection="vector">\r
  70                         <bind-xml name="qualifier"/>\r
  71                 </field>                                        \r
  72                 <field name="locations" type="jalview.datamodel.xdb.embl.EmblFeatureLocations" collection="vector">\r
  73                         <bind-xml name="location"/>\r
  74                 </field>\r
  75         </class>\r
  76         <class name="jalview.datamodel.DBRefEntry" verify-constructable="false">\r
  77                 <field name="accessionId" type="java.lang.String"><!-- set-method="setAccessionId" get-method="getAccessionId"> -->\r
  78                         <bind-xml name="primary" node="attribute"/>\r
  79                 </field>\r
  80                 <field name="source" type="java.lang.String"> <!--set-method="setSource" get-method="getSource"> -->\r
  81                         <bind-xml name="db" node="attribute"/>\r
  82                 </field>\r
  83                 <field name="version" type="string"><!-- set-method="setVersion" get-method="getVersion"> -->\r
  84                         <bind-xml name="secondary" node="attribute"/>\r
  85                 </field>\r
  86         </class>\r
  87         <class  name="jalview.datamodel.xdb.embl.Qualifier" verify-constructable="false">
  88                 <map-to xml="Qualifier"/>\r
  89                 <field name="name">\r
  90                         <bind-xml name="name" node="attribute"/>\r
  91                 </field>\r
  92                 <field name="value">
  93                         <bind-xml node="text"/>
  94                 </field>\r
  95         </class>\r
  96         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocations">\r
  97                 <map-to xml="location"/>\r
  98                 <field name="locationType" type="string">\r
  99                         <bind-xml name="type" node="attribute"/>\r
 100                 </field>\r
 101                 <field name="locationComplement" type="boolean">\r
 102                         <bind-xml name="complement" node="attribute"/>\r
 103                 </field>\r
 104                 <field name="locElements" type="jalview.datamodel.xdb.embl.EmblFeatureLocElement" collection="vector">\r
 105                         <bind-xml name="locationElement"/>\r
 106                 </field>\r
 107         </class>\r
 108         <class name="jalview.datamodel.xdb.embl.EmblFeatureLocElement">\r
 109                 <map-to xml="locationElement"/>\r
 110                 <field name="type" type="string">\r
 111                         <bind-xml name="type" node="attribute"/>\r
 112                 </field>\r
 113                 <field name="accession" type="string">\r
 114                         <bind-xml name="accession" node="attribute"/>                   \r
 115                 </field>\r
 116                 <field name="version" type="string">\r
 117                         <bind-xml name="version" node="attribute"/>\r
 118                 </field>\r
 119                 <field name="complement" type="boolean">\r
 120                         <bind-xml name="complement"/>\r
 121                 </field>\r
 122                 <field name="basePositions" type="jalview.datamodel.xdb.embl.BasePosition" collection="array">\r
 123                         <bind-xml name="basePosition" node="element"/>\r
 124                 </field>\r
 125         </class>\r
 126         <class name="jalview.datamodel.xdb.embl.BasePosition">
 127                 <map-to xml="basePosition"/>\r
 128                 <field name="type">
 129                         <bind-xml name="type" node="attribute"/>
 130                 </field>\r
 131                 <field name="pos">
 132                         <bind-xml node="text"/>\r
 133                 </field>\r
 134         </class>\r
 135 </mapping>\r